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Hi all, I'm currently trying a test run but get t...
# help
k
Hi all, I'm currently trying a test run but get this error:
Copy code
ERROR ~ No such variable: task

 -- Check script 'chipseq/modules/nf-core/samtools/faidx/main.nf' at line: 6 or see '.nextflow.log' file for more details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details
Updated faidx yesterday with nf-core/tools version 3.5.2 and I'm a bit lost 😄
m
Can you share some more code?
k
Sure, not entirely sure what, the .nextflow.log? I'm currently trying to update the modules in chipseq and use nextflow-25.10.4. This is at least the bit in the .nextflow.log that also drops an error:
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task: name=NFCORE_CHIPSEQ:CHIPSEQ:KHMER_UNIQUEKMERS; work-dir=null
  error [nextflow.exception.ProcessUnrecoverableException]: Path value cannot be null
Mar-12 08:37:23.885 [Task submitter] WARN  nextflow.script.ScriptBinding - Access to undefined parameter `clusterOptions` -- Initialise it to a default value eg. `params.clusterOptions = some_value`
Mar-12 08:37:23.904 [main] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
groovy.lang.MissingPropertyException: No such property: task for class: nextflow.script.dsl.ProcessDslV1
Possible solutions: class
	at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:68)
	at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.unwrap(IndyGuardsFiltersAndSignatures.java:163)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at Script_3c7c166bdf282990$_runScript_closure1$_closure6.doCall(Script_3c7c166bdf282990:6)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at groovy.lang.Closure.call(Closure.java:433)
	at groovy.lang.Closure.call(Closure.java:412)
	at org.codehaus.groovy.runtime.GStringUtil.writeToImpl(GStringUtil.java:89)
	at org.codehaus.groovy.runtime.GStringImpl.writeTo(GStringImpl.java:96)
	at groovy.lang.GString.toString(GString.java:121)
	at org.codehaus.groovy.runtime.GStringImpl.toString(GStringImpl.java:349)
	at nextflow.processor.LazyMap.resolveImpl(TaskConfig.groovy:707)
	at nextflow.processor.LazyMap.resolveImpl(TaskConfig.groovy)
	at nextflow.processor.LazyMap.resolve(TaskConfig.groovy:659)
	at nextflow.processor.LazyMap.getValue(TaskConfig.groovy:726)
	at nextflow.processor.LazyMap.get(TaskConfig.groovy:721)
	at nextflow.processor.TaskConfig.get(TaskConfig.groovy:153)
	at nextflow.processor.TaskConfig.getContainer(TaskConfig.groovy:438)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.processor.TaskRun.containerInfo0(TaskRun.groovy:714)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
	at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1339)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1094)
	at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnCurrentN(ScriptBytecodeAdapter.java:97)
	at nextflow.processor.TaskRun.this$dist$invoke$1(TaskRun.groovy)
	at nextflow.processor.TaskRun$3.methodMissing(TaskRun.groovy)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
	at groovy.lang.MetaClassImpl.invokeMissingMethod(MetaClassImpl.java:924)
	at groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1419)
	at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1341)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1094)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.processor.TaskRun$3.apply(TaskRun.groovy:703)
	at nextflow.processor.TaskRun$3.apply(TaskRun.groovy)
	at java.base/java.util.concurrent.ConcurrentHashMap.computeIfAbsent(ConcurrentHashMap.java:1708)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.processor.TaskRun.containerInfo(TaskRun.groovy:700)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.processor.TaskRun.getContainer(TaskRun.groovy:734)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.processor.TaskRun.isContainerEnabled(TaskRun.groovy:800)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.processor.TaskProcessor.formatTaskError(TaskProcessor.groovy:1317)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1131)
	at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.processor.TaskProcessor.handleException(TaskProcessor.groovy:1030)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
	at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1339)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1094)
	at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnCurrentN(ScriptBytecodeAdapter.java:97)
	at nextflow.processor.TaskProcessor.this$dist$invoke$1(TaskProcessor.groovy)
	at nextflow.processor.TaskProcessor$TaskProcessorInterceptor.methodMissing(TaskProcessor.groovy)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
	at groovy.lang.MetaClassImpl.invokeMissingMethod(MetaClassImpl.java:924)
	at groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1419)
	at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1341)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1094)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.processor.TaskProcessor$TaskProcessorInterceptor.onException(TaskProcessor.groovy:2458)
	at groovyx.gpars.dataflow.operator.DataflowProcessor.fireOnException(DataflowProcessor.java:331)
	at groovyx.gpars.dataflow.operator.DataflowProcessor.reportError(DataflowProcessor.java:293)
	at groovyx.gpars.dataflow.operator.DataflowProcessorActor.reportException(DataflowProcessorActor.java:125)
	at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:122)
	at groovyx.gpars.dataflow.operator.ForkingDataflowOperatorActor.access$001(ForkingDataflowOperatorActor.java:35)
	at groovyx.gpars.dataflow.operator.ForkingDataflowOperatorActor$1.run(ForkingDataflowOperatorActor.java:58)
	at java.base/java.util.concurrent.ThreadPoolExecutor$CallerRunsPolicy.rejectedExecution(ThreadPoolExecutor.java:2037)
	at java.base/java.util.concurrent.ThreadPoolExecutor.reject(ThreadPoolExecutor.java:833)
	at java.base/java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:1365)
	at groovyx.gpars.scheduler.DefaultPool.execute(DefaultPool.java:155)
	at groovyx.gpars.dataflow.operator.ForkingDataflowOperatorActor.startTask(ForkingDataflowOperatorActor.java:54)
	at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:108)
	at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43)
	at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293)
	at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30)
	at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93)
	at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
	at java.base/java.util.concurrent.ThreadPoolExecutor$CallerRunsPolicy.rejectedExecution(ThreadPoolExecutor.java:2037)
	at java.base/java.util.concurrent.ThreadPoolExecutor.reject(ThreadPoolExecutor.java:833)
	at java.base/java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:1365)
	at groovyx.gpars.scheduler.DefaultPool.execute(DefaultPool.java:155)
	at groovyx.gpars.util.AsyncMessagingCore.store(AsyncMessagingCore.java:99)
	at groovyx.gpars.actor.AbstractLoopingActor.send(AbstractLoopingActor.java:241)
	at groovyx.gpars.dataflow.operator.DataflowProcessorActor.send(DataflowProcessorActor.java:85)
	at groovyx.gpars.actor.AbstractLoopingActor.start(AbstractLoopingActor.java:173)
	at groovyx.gpars.dataflow.operator.DataflowProcessor.start(DataflowProcessor.java:139)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.processor.TaskProcessor$_start_closure14.doCall(TaskProcessor.groovy:592)
	at nextflow.processor.TaskProcessor$_start_closure14.doCall(TaskProcessor.groovy)
	at jdk.internal.reflect.GeneratedMethodAccessor145.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at groovy.lang.Closure.call(Closure.java:433)
	at groovy.lang.Closure.call(Closure.java:412)
	at nextflow.Session.callIgniters(Session.groovy:558)
	at nextflow.Session.fireDataflowNetwork(Session.groovy:550)
	at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:250)
	at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:139)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:429)
	at nextflow.cli.Launcher.run(Launcher.groovy:515)
	at nextflow.cli.Launcher.main(Launcher.groovy:675)
I submit the script by:
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nextflow \
    -DNXF_OPTS='-Xms1g -Xmx4g' \
    -Dnxf.pool.type=sync \
    -Djava.io.tmpdir=$TMPDIR \
    run ./chipseq/main.nf \
    --outdir ./output_test \
    --custom_config_base /{path}/pipelines/it_nfcore_hmgu_config \
    -profile test,hmgu,singularity \
    -resume
m
My guess is that the input channel has changed
👍 1
k
I'll have a look, likely that this has happened :)
Ok I think I found the issue but I'm a bit lost fixing it 😄 I currently try to change from 
CUSTOM_GETCHROMSIZES
to 
samtools/faidx
I want to compute the chromosome sizes If I try what is done in RNA-Seq 
SAMTOOLS_FAIDX(ch_fasta.map { item -> [ [:], item ] }, [ [:], [] ], true)
This gives me: Process 
NFCORE_CHIPSEQ:PREPARE_GENOME:SAMTOOLS_FAIDX
declares 2 inputs but was called with 3 arguments. I'm a bit lost 😄 the ch_fasta only contains the ref genome
Ok found the issue. samtools/faidx was updated and now takes only a single tuple, while the older version, also in RNASEQ uses an older version.
m
yeah, that's multiple changes all at once
k
Sorted it. Thanks for pointing to the error!
m
You're too nice, you solved it all on your on
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